ntLink

ntLink scaffolds draft genome assemblies using long-read sequencing data and minimizer-based mappings to infer ordering and orientation, detect overlaps, and perform gap-filling.

Key Features:

• Minimizer-Based Mappings: Employs minimizer-based mappings rather than full read alignments to infer the optimal order and orientation of input sequences into scaffolds.
• Overlap Detection and Gap-Filling: Detects overlaps between sequences and fills gaps within scaffolds to increase contiguity.
• In-Code Scaffolding Iterations: Supports iterative in-code scaffolding to refine assemblies across multiple rounds.
• Modularity and Flexibility: Provides modular execution modes to adapt scaffolding workflows to different project requirements.
• Downstream Applications: Produces lightweight minimizer mappings usable for misassembly detection and genome assembly correction, including workflows involving Tigmint-long.

Scientific Applications:

• Genome Scaffolding: Scaffolds draft genome assemblies and aids resolution of complex repetitive regions using long reads and minimizer mappings.
• Misassembly Detection: Identifies potential misassemblies via minimizer-based mapping patterns for subsequent correction.
• Gap-Filling: Performs gap-filling to improve assembly completeness for downstream analyses.
• Assembly Correction: Generates long-read-to-contig mappings that can be used in assembly correction workflows such as Tigmint-long.

Methodology:

Uses long-read sequencing data and a minimizer-based mapping approach to map reads/contigs, infer ordering and orientation, detect overlaps, perform gap-filling, support iterative in-code scaffolding, and generate long-read-to-contig mappings for downstream correction with tools like Tigmint-long.